OpenMM

A set of tutorials that demonstrate how to use NanoVer to run interactive molecular dynamics simulations using OpenMM directly.

The Jupyter notebook tutorials that demonstrate how to run interactive molecular dynamics simulations by interfacing NanoVer with OpenMM directly can be found in the examples folder of the GitHub repository. It contains:

• openmm_polyalanine: A notebook that demonstrates how to set up an interactive OpenMM simulation from scratch with NanoVer, use features of OpenMM in conjunction with NanoVer, and record & playback simulations directly using NanoVer.

• openmm_nanotube: A notebook that demonstrates how to interact with an OpenMM NanoVer simulation using a python client.

• openmm_neuraminidase: A notebook that demonstrates how to set up an interactive OpenMM simulation from scratch with NanoVer and change the visualisations of different atom selections for a protein-ligand system.